Silver nanoparticles coated by a layer of gold (Ag@Au) have received much attention because of their potential application as ultra sensitive probes for the detection of biologically important molecules such as DNA, proteins, amino acids and many others. However, the ability to control the size, shape, and monodispersity of the Ag@Au structure has met with limited success. In our own research we have addressed this challenge by creating an aqueous wet chemical synthesis technique towards size and shape controllable Ag@Au nanoparticles. These materials are highly interesting because of the tunable silver core size, and the tunable gold shell thickness, opening many avenues to the modification of the particle properties in terms of bio-molecular sensing. The resulting nanoparticle probes were functionalized with two complementary stranded DNA oligonucleotides. When combined, the complementary strands hybridized, causing the Ag@Au nanoparticles to assemble into large nano-structures. The presence of the oligonucleotide was confirmed through a series of techniques including UV-Vis and Raman spectroscopy, as well as TEM, XPS, DLS, and many others. The results reflect the role that the nanoparticle physical properties play in the detection of the bio-molecules, as well as elucidate the characteristics of the bio-molecule/nanoparticle interaction.